Biology & Genomics

Query genomic databases and run BLAST-style lookups with the gget CLI and Python

Browse a gateway of over 400 genomics and bioinformatics skills

Search ChEMBL and check drug-likeness and interactions for candidate molecules

Run and monitor Seqera bioinformatics pipelines through the Composio Rube MCP server

Estimate intracellular metabolic fluxes from carbon-13 isotope tracing data

Design protein assays, estimate costs and submit sequences to the Adaptyv Bio Foundry

Look up AlphaGenome effects and scores for GRCh38 single-nucleotide variants

Plan and document ICH and USP validation of HPLC, LC-MS and other analytical methods

Read, write and slice annotated single-cell matrices in h5ad and Zarr files

Infer gene regulatory networks from expression data with GRNBoost2 and GENIE3

Automate Benchling registry, inventory, ELN and warehouse tasks with its SDK and API

Organize, validate and convert brain imaging datasets to the BIDS standard

Parse FASTA, GenBank and PDB files and query NCBI with Biopython workflows

Pull protein, pathway and chemical annotations from UniProt, KEGG and ChEMBL

Turn bulk RNA-seq FASTQ or quant output into validated gene-level count tables

Run CellProfiler pipelines for nuclear segmentation, cell counts and fluorescence QC

Query CZ CELLxGENE Census for single-cell expression, metadata and reference atlases

Run flux balance, knockout and sampling analyses on metabolic models with COBRApy

Parse, standardize and featurize SMILES molecules with a friendly RDKit wrapper

Predict transcriptome-wide spatial expression from H&E histology tiles

Convert BAM to bigWig and plot QC, heatmaps and profiles for ChIP-seq and ATAC-seq

Analyze DepMap cancer dependency data for gene effects, biomarkers and drug sensitivity

Predict protein-ligand binding poses with DiffDock for docking and virtual screening

Build and run reproducible genomics workflows on DNAnexus with dx CLI and dxpy

Generate proteins, compute ESMC embeddings and fold structures with the ESM SDK

Analyze, compare and draw phylogenetic trees with ETE for taxonomy and reconciliation

Read, inspect and write Flow Cytometry Standard FCS files and export event tables

Compensate, gate and transform flow cytometry data and reproduce FlowJo gate counts

Validate BED genomic interval files and plan Region2Vec or scEmbed embedding runs

Convert genomic coordinates between BED, GFF, VCF and assembly conventions safely

Predict promoters, splice sites and expression from DNA sequence with hosted models

Query bioinformatics databases for gene info, BLAST, structures and enrichment

Choose a Ginkgo Cloud Lab protocol, check prices and prepare an order

Scan protein sequons and plan glycan engineering and shielding workflows

Count genomic interval overlaps, build coverage and tokenize fragments with Gtars

Extract tissue tiles from whole-slide histology images and normalize H&E stains

Connect to LabArchives ELN and Inventory APIs with signed requests

Track lineage and validate schemas for biological datasets with LaminDB

Build and deploy bioinformatics workflows on Latch with the Python SDK and Nextflow

Analyze pooled CRISPR screen reads and rank gene hits with effect sizes and FDR

Triage compound libraries with drug-likeness rules, PAINS alerts and complexity filters

Set up, run and analyze molecular dynamics simulations with OpenMM and MDAnalysis

Query the NCATS Translator ARAX knowledge graph for typed biomedical relationships

Preprocess physiological signals and compute variability and complexity with NeuroKit2

Sort and curate Neuropixels spikes with SpikeInterface, Kilosort4 and drift correction

Convert neuroscience recordings to NWB files with metadata, clock alignment and validation

Inventory, export and reviewed-write microscopy data on an OMERO server with omero-py

Find 1000 Genomes individuals who carry variants matching gene or region criteria

Map free-text scientific labels to ontology term IDs and validate existing CURIEs